I still see no mention of the Endar Spire being a flagship of any kind. Closest term I see is Capital ship, which =/= flagship. But I guess my comment about this was a minor terminology thing that I picked up on more than anything. It's not really important, even by our nit picky, fan-boy standards.
And simply because the crawl says that the fleet was engaging Malak's doesn't mean they were sent there to do so. In fact, Carth said as much, saying that "[they] didn't choose that battle, anyway, it got forced on [them]". They could very well have been on a supply run or patrol, and been ambushed.
As far as Wookiepedia's lack of mention of other ships is concerned; not only is Wookiepedia one of the least credible sources out there, but it can by no means retcon information from the game itself - which clearly states that a fleet was engaged in the battle of Taris.
Also remember that we only see a minuscule part of Taris. The entire planet could have been riddled with escape pods, easily.